I able to load libpcap.dylib which is confusing cause I can't figure out the actual file location. Doing find / -name libpcap.A.dylib or libpcap.dylib says no such file.
Also finder search with libpcap just results in libpcap.A.tbd and libpcap.rb.
libpcap.A.tbd shows "Install location /usr/lib/libpcap.A.dylib", but it does not actually exist there.
I wanted to locate the actual dylib file cause I running into issue with being able to import function, So I wanted to check file to make sure I have function names correct.
So I wanted to check file to make sure I have function names correct.
The first thing to check is the pcap man page - from the command line, it'd be
man pcap
It's a bit long, but it should mention all the functions available in libpcap; it may be easier than
nm /usr/lib/libpcap.dylib | egrep ' T '
(and doesn't require you to remember that the leading underscores in the output of that command are NOT part of the name of the function, they're a leftover from ancient UNIX history).
Where is libpcap.dylib?
/usr/lib/libpcap.A.dylib. /usr/lib/libpcap.dylib is a symbolic link to it.
Related
I'm new in Bioinformatics and Biopython, so I have some difficulties with it.
I was reading the Biopython (SeqIO) documentation, but when I try to execute some SeqIO.parse() commands I get FileNotFoundError.
For example, I want to get "example.fasta" file (which I don't have it on my PC). I try to do it with this command:
for record in SeqIO.parse("example.fasta", "fasta"):
print(record.id)
But, all I get is FileNotFoundError: [Errno 2] No such file or directory
Can someone help me with this?
My understanding is that FileNotFoundError occurs when the code tries to open a file on your computer and does not find it.
This can happen either because you simply do not have this file, or you gave the name with a typo, or the path to the file is not correct (This is an important notion: the path to the file should be absolute, or relative to the current working directory (usually the one from which you executed the python script)).
As suggested in the comments to your question, you seem to be expecting SeqIO.parse to get the file for you. This is not the case. The first argument you give to this function (in the example "example.fasta") is the path to an existing file that you want to "parse", that is, interpret its information content and make this content available to the rest of your program in a convenient form.
So in order to get this example working, you first need to get a fasta file. If you do not already have one, you can download some manually from genbank, or find one in the biopython installation (if you installed it from source and know where the source code is located), for instance in Tests/Quality/example.fasta.
Oracle's sqlldr defaults to a .dat extension. That I want to override. I don't like to rename the file. When googled get to know few answers to use . like data='fileName.' which is not working. Share your ideas, please.
Error message is fileName.dat is not found.
Sqlloder has default extension for all input files data,log,control...
data= .dat
log= .log
control = .ctl
bad =.bad
PARFILE = .par
But you have to pass filename without apostrophe and dot
sqlloder pass/user#db control=control data=data
sqloader will add extension. control.ctl data.dat
Nevertheless i do not understand why you do not want to specify extension?
You can't, at least in Unix/Linux environments. In Windows you can use the trailing period trick, specifying either INFILE 'filename.' in the control file or DATA=filename. on the command line. WIndows file name handling allows that; you can for instance do DIR filename. at a command prompt and it will list the file with no extension (as will DIR filename). But you can't do that with *nix, from a shell prompt or anywhere else.
You said you don't want to copy or rename the file. Temporarily renaming it might be the simplest solution, but as you may have a reason not to do that even briefly you could instead create a hard or soft link to the file which does have an extension, and use that link as the target instead. You could wrap that in a shell script that takes the file name argument:
# set variable from correct positional parameter; if you pass in the control
# file name or other options, this might not be $1 so adjust as needed
# if the tmeproary file won't be int he same directory, need to be full path
filename=$1
# optionally check file exists, is readable, etc. but overkill for demo
# can also check temporary file does not already exist - stop or remove
# create soft link somewhere it won't impact any other processes
ln -s ${filename} /tmp/${filename##*/}.dat
# run SQL*Loader with soft link as target
sqlldr user/password#db control=file.ctl data=/tmp/${filename##*/}.dat
# clean up
rm -f /tmp/${filename##*/}.dat
You can then call that as:
./scriptfile.sh /path/to/filename
If you can create the link in the same directory then you only need to pass the file, but if it's somewhere else - which may be necessary depending on why renaming isn't an option, and desirable either way - then you need to pass the full path of the data file so the link works. (If the temporary file will be int he same filesystem you could use a hard link, and you wouldn't have to pass the full path then either, but it's still cleaner to do so).
As you haven't shown your current command line options you may have to adjust that to take into account anything else you currently specify there rather than in the control file, particularly which positional argument is actually the data file path.
I have the same issue. I get a monthly download of reference data used in medical application and the 485 downloaded files don't have file extensions (#2gb). Unless I can load without file extensions I have to copy the files with .dat and load from there.
I'm having trouble installing Homebrew, and it looks like the problem (invalid byte sequence in UTF-8 (ArgumentError) error message) is due to a fault in my PATH. when I run echo $PATH, I get the following (be sure to scroll to the far right in the code block below to see the fault):
/usr/local/mysql/bin:/opt/subversion/bin/:/usr/local/bin:/usr/local/sbin:/usr/bin:/bin:/usr/sbin:/sbin:PATH=/usr/local/share/python:$PATH:PATH=/usr/local/share/npm/bin:$PATH:export PATH��:/usr/local/git/bin
I have no idea where those strange characters just before the /usr/local/git/bin path are coming from. I'm using bash (tried zshell, same problem). I can't find where this coming from. my .bash_profile file looks clean, too.
Examine your ~/.profile, ~/.bash_profile, and ~/.bashrc files. It is also possible that these values are being set in /etc/profile or other system-wide files, but the nature of the errors is such that I would assume they are the result of your own manual edits of your personal files. You're the best judge to decide what you may have changed and when.
Look for entries such as the following:
PATH='/usr/local/share/python:$PATH'
PATH='PATH=/usr/local/share/npm/bin:$PATH'
PATH='export PATH��:/usr/local/git/bin'
They should instead look like
PATH=/usr/local/share/python:$PATH
PATH=/usr/local/share/npm/bin:$PATH
PATH=$PATH:/usr/local/git/bin
# Not strictly necessary -- PATH is already exported
export PATH
See a pattern? These all add a value to PATH by setting it to prefix:$PATH or $PATH:suffix where the new prefix or suffix is the directory where you have installed a local package. Whether the new value should be a prefix or a suffix is probably of little consequence -- except if you are trying to override a system version (say, your /usr/local/git is installed because /usr/bin/git is too old -- then, it's important that your local version comes first in the PATH). There is also a minuscule speed difference the first time you run a command; the shell has to look in more places before finding it if it's at the end of the PATH.
The difference in quoting is significant -- PATH=$PATH:suffix expands to the old value of PATH with :suffix added on, whereas PATH='$PATH:suffix' replaces the old value of PATH with the literal string $PATH with :suffix added on. You're lucky none of this has ended up replacing your original PATH completely, which would render your shell by and large inoperable (at least until you discover that you have to use /bin/ls instead of just ls).
I try to find a file with locate command.
It behaves itself some strange with patterns, at least not like ls or find commands.
I do the following:
sh#sh:~$ locate rhythmdb
/home/sh/.local/share/rhythmbox/rhythmdb.xml
sh#sh:~$ locate "rhyth*"
sh#sh:~$ locate 'rhyth*'
sh#sh:~$ locate rhyth*
(Screenshot)
In my humble opinion it should find when asterisk is used too, but it doesn't.
What can be wrong?
From man locate:
If --regex is not specified, PATTERNs can contain globbing characters. If any
PATTERN contains no globbing characters, locate behaves as if the pattern
were \*PATTERN*.
Hence, when you issue
locate rhyth*
locate will not find it, because there are no files that match this pattern: since there's a glob character, locate will really try to match (in regex): ^rhyth.* and there are obviously no such matches (on full paths).
In your case, you could try:
locate "/home/sh/.local/share/rhythmbox/rhyth*"
or
locate '/rhyth' # equivalent to locate '*/rhyth*'
But that's not very good, is it?
Now, look at the first option in man locate:
-b, --basename
Match only the base name against the specified patterns. This
is the opposite of --wholename.
Hurray! the line:
locate -b "rhyth*"
should work as you want it to: locate a file with basename matching (in regex): ^rhyth.*
Hope this helps.
Edit. To answer your comment: if you want to locate all jpg files in folder /home/sh/music/, this should do:
locate '/home/sh/music/*.jpg'
(no -b here, it wouldn't work). Notice that this will show all jpg files that are in folder /home/sh/music and also in its subfolders. You could be tempted to use the -i flag (ignore case) so that you'll also find those that have the uppercase JPG extension:
locate -i '/home/sh/music/*.jpg'
Edit 2. Better to say it somewhere: the locate command works with a database — that's why it can be much faster than find. If you have recent files, they won't be located and if you delete some files, they might still be located. If you're in this case (which might be the purpose of your other comment), you must update locate's database: as root, issue:
updatedb
Warning. The command updatedb might take a few minutes to complete, don't worry.
Okay so here is what I want to do. I want to add a print option that prints whatever the user's document is to a PDF and adds some headers before sending it off to a device.
I guess my questions are: how do I add a virtual "printer" driver for the user that will launch the application I've been developing that will make the PDF (or make the PDF and launch my application with references to the newly generated PDF)? How do I interface with CUPS to generate the PDF? I'm not sure I'm being clear, so let me know if more information would be helpful.
I've worked through this printing with CUPS tutorial and seem to get everything set up okay, but the file never seems to appear in the appropriate temporary location. And if anyone is looking for a user-end PDF-printer, this cups-pdf-for-mac-os-x is one that works through the installer, however I have the same issue of no file appearing in the indicated directory when I download the source and follow the instructions in the readme. If anyone can get either of these to work on a mac through the terminal, please let me know step-by-step how you did it.
The way to go is this:
Set up a print queue with any driver you like. But I recommend to use a PostScript driver/PPD. (A PostScript PPD is one which does not contain any *cupsFilter: ... line.):
Initially, use the (educational) CUPS backend named 2dir. That one can be copied from this website: KDE Printing Developer Tools Wiki. Make sure when copying that you get the line endings right (Unix-like).
Commandline to set up the initial queue:
lpadmin \
-p pdfqueue \
-v 2dir:/tmp/pdfqueue \
-E \
-P /path/to/postscript-printer.ppd
The 2dir backend now will write all output to directory /tmp/pdfqueue/ and it will use a uniq name for each job. Each result should for now be a PostScript file. (with none of the modifications you want yet).
Locate the PPD used by this queue in /etc/cups/ppd/ (its name should be pdfqueue.ppd).
Add the following line (best, near the top of the PPD):
*cupsFilter: "application/pdf 0 -" (Make sure the *cupsFilter starts at the very beginning of the line.) This line tells cupsd to auto-setup a filtering chain that produces PDF and then call the last filter named '-' before it sends the file via a backend to a printer. That '-' filter is a special one: it does nothing, it is a passthrough filter.
Re-start the CUPS scheduler:sudo launchctl unload /System/Library/LaunchDaemons/org.cups.cupsd.plist
sudo launchctl load /System/Library/LaunchDaemons/org.cups.cupsd.plist
From now on your pdfqueue will cause each job printed to it to end up as PDF in /tmp/pdfqueue/*.pdf.
Study the 2dir backend script. It's simple Bash, and reasonably well commented.
Modify the 2dir in a way that adds your desired modifications to your PDF before saving on the result in /tmp/pdfqueue/*.pdf...
Update: Looks like I forgot 2 quotes in my originally prescribed *cupsFilter: ... line above. Sorry!
I really wish I could accept two answers because I don't think I could have done this without all of #Kurt Pfeifle 's help for Mac specifics and just understanding printer drivers and locations of files. But here's what I did:
Download the source code from codepoet cups-pdf-for-mac-os-x. (For non-macs, you can look at http://www.cups-pdf.de/) The readme is greatly detailed and if you read all of the instructions carefully, it will work, however I had a little trouble getting all the pieces, so I will outline exactly what I did in the hopes of saving someone else some trouble. For this, the directory with the source code is called "cups-pdfdownloaddir".
Compile cups-pdf.c contained in the src folder as the readme specifies:
gcc -09 -s -lcups -o cups-pdf cups-pdf.c
There may be a warning: ld: warning: option -s is obsolete and being ignored, but this posed no issue for me. Copy the binary into /usr/libexec/cups/backend. You will likely have to the sudo command, which will prompt you for your password. For example:
sudo cp /cups-pdfdownloaddir/src/cups-pdf /usr/libexec/cups/backend
Also, don't forget to change the permissions on this file--it needs root permissions (700) which can be changed with the following after moving cupd-pdf into the backend directory:
sudo chmod 700 /usr/libexec/cups/backend/cups-pdf
Edit the file contained in /cups-pdfdownloaddir/extra/cups-pdf.conf. Under the "PDF Conversion Settings" header, find a line under the GhostScript that reads #GhostScript /usr/bin/gs. I did not uncomment it in case I needed it, but simply added beneath it the line Ghostscript /usr/bin/pstopdf. (There should be no pre-cursor # for any of these modifications)
Find the line under GSCall that reads #GSCall %s -q -dCompatibilityLevel=%s -dNOPAUSE -dBATCH -dSAFER -sDEVICE=pdfwrite -sOutputFile="%s" -dAutoRotatePage\
s=/PageByPage -dAutoFilterColorImages=false -dColorImageFilter=/FlateEncode -dPDFSETTINGS=/prepress -c .setpdfwrite \
-f %s Again without uncommenting this, under this I added the line GSCall %s %s -o %s %s
Find the line under PDFVer that reads #PDFVer 1.4 and change it to PDFVer, no spaces or following characters.
Now save and exit editing before copying this file to /etc/cups with the following command
sudo cp cups-pdfdownloaddir/extra/cups-pdf.conf /etc/cups
Be careful of editing in a text editor because newlines in UNIX and Mac environments are different and can potentially ruin scripts. You can always use a perl command to remove them, but I'm paranoid and prefer not to deal with it in the first place.
You should now be able to open a program (e.g. Word, Excel, ...) and select File >> Print and find an available printer called CUPS-PDF. Print to this printer, and you should find your pdfs in /var/spool/cups-pdf/yourusername/ by default.
*Also, I figured this might be helpful because it helped me: if something gets screwed up in following these directions and you need to start over/get rid of it, in order to remove the driver you need to (1) remove the cups-pdf backend from /usr/libexec/cups/backend (2) remove the cups-pdf.conf from /etc/cups/ (3) Go into System Preferences >> Print & Fax and delete the CUPS-PDF printer.
This is how I successfully set up a pdf backend/filter for myself, however there are more details, and other information on customization contained in the readme file. Hope this helps someone else!